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Calcium in PDB 3u39: Crystal Structure of the Apo Bacillus Stearothermophilus Phosphofructokinase

Enzymatic activity of Crystal Structure of the Apo Bacillus Stearothermophilus Phosphofructokinase

All present enzymatic activity of Crystal Structure of the Apo Bacillus Stearothermophilus Phosphofructokinase:
2.7.1.11;

Protein crystallography data

The structure of Crystal Structure of the Apo Bacillus Stearothermophilus Phosphofructokinase, PDB code: 3u39 was solved by R.Mosser, M.C.M.Reddy, J.B.Bruning, J.C.Sacchettini, G.D.Reinhart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.51 / 2.79
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 201.909, 113.383, 76.627, 90.00, 104.03, 90.00
R / Rfree (%) 19.9 / 26

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Apo Bacillus Stearothermophilus Phosphofructokinase (pdb code 3u39). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of the Apo Bacillus Stearothermophilus Phosphofructokinase, PDB code: 3u39:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3u39

Go back to Calcium Binding Sites List in 3u39
Calcium binding site 1 out of 5 in the Crystal Structure of the Apo Bacillus Stearothermophilus Phosphofructokinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Apo Bacillus Stearothermophilus Phosphofructokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca320

b:85.1
occ:1.00
 O B:HOH394 3.1 46.6 1.0
O A:HOH393 4.0 38.4 1.0
CB A:ASN144 4.5 30.8 1.0
CG A:ASN144 4.7 31.4 1.0
CG2 A:THR257 4.8 29.8 1.0
CG2 B:THR257 4.8 29.6 1.0
CG B:ASN144 4.8 34.0 1.0
OD1 B:ASN144 4.9 28.7 1.0
CB B:ASN144 4.9 34.7 1.0
ND2 A:ASN144 4.9 32.2 1.0

Calcium binding site 2 out of 5 in 3u39

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Calcium binding site 2 out of 5 in the Crystal Structure of the Apo Bacillus Stearothermophilus Phosphofructokinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Apo Bacillus Stearothermophilus Phosphofructokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca321

b:69.0
occ:1.00
 OD2 A:ASP155 3.1 40.1 1.0
OD1 A:ASP155 3.4 34.3 1.0
N D:GLY64 3.4 35.9 1.0
CG A:ASP155 3.6 36.8 1.0
CA D:ARG63 4.1 34.1 1.0
CA D:GLY64 4.2 33.3 1.0
C D:ARG63 4.2 33.1 1.0
O A:HOH398 4.3 35.7 1.0
CG D:ARG63 4.4 48.6 1.0
O D:HIS62 4.5 34.1 1.0
N D:SER255 4.7 28.9 1.0
C D:GLY254 4.7 28.3 1.0
O D:GLY254 4.8 25.6 1.0
NE2 B:HIS62 4.8 40.6 1.0
CB D:ARG63 4.9 42.3 1.0
O D:HOH381 4.9 48.7 1.0
CD2 B:HIS62 4.9 37.8 1.0
CA D:SER255 4.9 24.7 1.0
C D:GLY64 5.0 32.1 1.0
O D:GLY64 5.0 35.2 1.0

Calcium binding site 3 out of 5 in 3u39

Go back to Calcium Binding Sites List in 3u39
Calcium binding site 3 out of 5 in the Crystal Structure of the Apo Bacillus Stearothermophilus Phosphofructokinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Apo Bacillus Stearothermophilus Phosphofructokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca320

b:73.3
occ:1.00
 OD2 B:ASP155 3.3 42.7 1.0
OD1 B:ASP155 3.4 33.8 1.0
N C:GLY64 3.5 36.0 1.0
CG B:ASP155 3.8 37.2 1.0
CA C:ARG63 4.0 37.9 1.0
C C:ARG63 4.3 37.0 1.0
N C:SER255 4.4 24.4 1.0
O C:HIS62 4.4 30.6 1.0
CA C:GLY64 4.4 33.5 1.0
CB C:ARG63 4.5 37.9 1.0
CG C:ARG63 4.6 52.3 1.0
CA C:SER255 4.7 29.0 1.0
C C:GLY254 4.7 27.0 1.0
CB C:SER255 4.8 26.3 1.0
NE2 A:HIS62 4.9 41.0 1.0

Calcium binding site 4 out of 5 in 3u39

Go back to Calcium Binding Sites List in 3u39
Calcium binding site 4 out of 5 in the Crystal Structure of the Apo Bacillus Stearothermophilus Phosphofructokinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Apo Bacillus Stearothermophilus Phosphofructokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca320

b:73.7
occ:1.00
 OD1 C:ASP155 3.3 42.3 1.0
OD2 C:ASP155 3.4 39.8 1.0
N B:GLY64 3.6 37.1 1.0
CG C:ASP155 3.7 41.2 1.0
O C:HOH351 3.8 48.4 1.0
CA B:ARG63 4.2 37.4 1.0
N B:SER255 4.4 26.1 1.0
CA B:GLY64 4.4 35.0 1.0
C B:ARG63 4.4 35.3 1.0
O B:HIS62 4.5 28.7 1.0
C B:GLY254 4.6 27.7 1.0
CG B:ARG63 4.6 45.6 1.0
CA B:SER255 4.7 28.0 1.0
CE1 D:HIS62 4.8 47.5 1.0
CB B:ARG63 4.8 40.5 1.0
CB B:SER255 4.8 26.1 1.0
O B:GLY254 4.8 31.6 1.0
ND1 D:HIS62 5.0 41.1 1.0

Calcium binding site 5 out of 5 in 3u39

Go back to Calcium Binding Sites List in 3u39
Calcium binding site 5 out of 5 in the Crystal Structure of the Apo Bacillus Stearothermophilus Phosphofructokinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Apo Bacillus Stearothermophilus Phosphofructokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca321

b:75.5
occ:1.00
 OD2 D:ASP307 3.1 43.2 1.0
O C:ASN289 3.2 41.6 1.0
NH2 C:ARG266 3.2 35.7 1.0
O C:HOH389 3.9 47.8 1.0
CZ C:ARG266 4.1 44.6 1.0
NH1 C:ARG266 4.1 44.1 1.0
CG D:ASP307 4.1 36.4 1.0
C C:ASN289 4.3 43.5 1.0
O C:HOH397 4.3 43.7 1.0
ND2 C:ASN289 4.3 39.7 1.0
O C:HOH375 4.4 50.1 1.0
OD1 C:ASN289 4.4 45.0 1.0
CG C:ASN289 4.4 38.0 1.0
CB D:ASP307 4.6 33.3 1.0
CA C:GLN290 4.9 37.2 1.0

Reference:

R.Mosser, M.C.Reddy, J.B.Bruning, J.C.Sacchettini, G.D.Reinhart. Structure of the Apo Form of Bacillus Stearothermophilus Phosphofructokinase. Biochemistry V. 51 769 2012.
ISSN: ISSN 0006-2960
PubMed: 22212099
DOI: 10.1021/BI201548P
Page generated: Tue Jul 8 17:08:49 2025

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